Class BondSearch

java.lang.Object
  |
  +--BondSearch

public class BondSearch

extends java.lang.Object

Finds bonds between Atoms in a Molecule

Inner Class Summary

static class

BondSearch.GridSearchPair GridSearchPair holds information for 2 atoms that share a bond

Constructor Summary

BondSearch()

Method Summary

static int[][]	bondSearch(Molecule molec, float cutoff) Determines the actual bonds for each atom in the molecule
static BondSearch.GridSearchPair	gridSearch(Molecule molec, float pairDist) Creates GridSearchPairs to determine closeness of atoms for bond search Here's how it works: gridSearch() divides the space that the molecule occupies into a 3-d grid of cubes, or gridboxes.
static int[][]	makeNeighborCheckList(int numAtoms, int xb, int yb, int zb) Creates a list of which neighbors to check for which boxes

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

BondSearch

public BondSearch()

Method Detail

makeNeighborCheckList

public static int[][] makeNeighborCheckList(int numAtoms,
                                            int xb,
                                            int yb,
                                            int zb)

Creates a list of which neighbors to check for which boxes

Parameters:

numAtoms - the number of atoms in the molecule

xb - the number of boxes in the x direction

yb - the number of boxes in the y direction

zb - the number of boxes in the z direction

Returns:

a 2d integer array lising the gridboxes to check for each atom

gridSearch

public static BondSearch.GridSearchPair gridSearch(Molecule molec,
                                                   float pairDist)

Creates GridSearchPairs to determine closeness of atoms for bond search Here's how it works: gridSearch() divides the space that the molecule occupies into a 3-d grid of cubes, or gridboxes. For each gridbox, it determines which atoms are in that box. It also determines which gridboxes neighbor that box, and should be checked for neighboring atoms. This step allows large molecules to be loaded faster, since atoms that are far apart won't be checked for bonds.

Parameters:

molec - Molecule to determine grid for

pairDist - dimension of a single grid box

Returns:

a GridSearchPair of all the atom pairs close enough to be searched for bonds

bondSearch

public static int[][] bondSearch(Molecule molec,
                                 float cutoff)

Determines the actual bonds for each atom in the molecule

Parameters:

molec - the Molecule for which to determine bonds

cutoff - distance to check for cutoff

Returns:

a 2d integer array that lists the neighboring atoms for each atom